PRIMERS

If a single primer is producing product then it is functioning as both
an unstream and downstream primer (or forward and reverse primer); the
problem is with your design of the primer. A cheap way to check where
your primer may be binding is to have the sequence of your expected
fragment in a word processing package (like MS Word) and then use the
'Find' option to search the sequence using a small number of the bases
from the 3' end of the primer eg 5'> ....ATgCtggCTAC>3' then have 'Find'
look for CTAC sites (and CATC sites for the reverse phase).... something
like looking for restriction enzyme cuts. This may give you possible
sites that are binding from which you can calculate the fragment
lengths, compare to your gel and deduce the putative binding. In the
end you are still going to have to redesign the primers.
--
Patrick HJ Falckh PhD # #
Key Centre for Applied & Nutritional Toxicology # # # # #
RMIT - City Campus # Q Q #
GPO Box 2467V, Melbourne Vic 3001 # o #
# ~ #
Telephone : 03 9660 3136 ##<->##
Fax No. : 03 9663 6087 # #
Email : p.falckh at rmit.edu.au # # # #
## ##
"No matter how tall your grandfather # \/ #
was, you have to do your own growing" # /\ #
ooO Ooo